<br><br><div class="gmail_quote">2010/10/4 Jochen Hub <span dir="ltr"><<a href="mailto:jochen@xray.bmc.uu.se">jochen@xray.bmc.uu.se</a>></span><br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div><div></div><div class="h5">šOn 10/2/10 Oct 2,10:51 PM, ðÅÔÒ ðÏÐÏ× wrote:<br>
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Hello, dears gmx-users!<br>
<br>
I posted a message, but didn't get a response, it was my first one, so may be I did something wrong. Anyway, here it is:<br>
<br>
I've already run md and got pmf and it's correct. But I want to get not just a pmf of total force, but several profiles each of which corresponds to the different components. For example, one pmf - protein-protein interactions, another - protein-solvent interactions. Or another, one pmf corresponds to electrostatic, another to VdW etc.<br>
Should I change a program's code? If so, tell me please in what exactly program?<br>
Or may be gromacs have similar functions? Or is the another way to split pmf?<br>
</blockquote></div></div>
Hi, what we did some years ago (Hub and de Groot, Does CO2 permeate through aquaporin-1, Biophys J 91, 842-848 (2006)), we used the energy file to decompose the potential (that is the enthalpic contribution to the PMF) into solute-water, solute-protein interactions, etc. You would have to make a tpr file with different energy groups and then do a rerun. Note that we do not decompose the mean force with that procedure though.<br>
<br>
I hope this helps.<br>
<br>
Cheers,<br>
<br>
Jochen<div class="im"><br>
<br>
<br>
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<br>
Thank you for your attention!<br>
<br>
<br>
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Dr. Jochen Hub<br>
Computational and Systems Biology<br>
Dept. of Cell& šMolecular Biology<br>
Uppsala University. Box 596, 75124 Uppsala, Sweden.<br>
Phone: +46-18-4715056 Fax: +46-18-511755<br>
<a href="http://xray.bmc.uu.se/%7Ejochen/index.html" target="_blank">http://xray.bmc.uu.se/~jochen/index.html</a><br>
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</font></blockquote></div>Thank you for your response and for the article! <br>I think it is what I want. But could you explain it more detailed? I mean, how did you decompose the potential?<br>